Funseq2 - Revision history

Public: /* Contact */

2017-10-19T00:05:59Z

Contact

← Older revision		Revision as of 00:05, 19 October 2017
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	=Contact=		=Contact=
	~~Yao Fu at yao~~ DOT fu AT yale DOT edu		shaoke DOT lou AT yale DOT edu

Public: /* Docker Image Usage */

2015-07-16T21:23:11Z

Docker Image Usage

← Older revision		Revision as of 21:23, 16 July 2015
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	Please download Docker at https://www.docker.com/		Please download Docker at https://www.docker.com/
	* Export docker image to your computer:		* Export docker image to your computer:
	$ docker load -i ~~funseq2_docker_image~~.tar		$ docker load -i funseq2-docker-image.tar
	* Run docker container		* Run docker container
	$ ./funseq2-docker.sh		$ ./funseq2-docker.sh

Public: /* Docker Image Usage */

2015-07-16T21:08:50Z

Docker Image Usage

← Older revision		Revision as of 21:08, 16 July 2015
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	Please download Docker at https://www.docker.com/		Please download Docker at https://www.docker.com/
	* Export docker image to your computer:		* Export docker image to your computer:
	$ docker load ~~< funseq2~~-~~docker~~.tar		$ docker load -i funseq2_docker_image.tar
	* Run docker container		* Run docker container
	~~$ docker run -t -i -v path_to_Data_Context_on_your_computer:/funseq2/data_context ouruser/funseq /bin/bash~~		$ ./funseq2-docker.sh
	~~$ cd funseq2~~
	$ ./funseq2.sh

	=Building data context=		=Building data context=

Public: /* Docker Image Usage */

2015-06-11T16:40:31Z

Docker Image Usage

← Older revision		Revision as of 16:40, 11 June 2015
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	$ docker load < funseq2-docker.tar		$ docker load < funseq2-docker.tar
	* Run docker container		* Run docker container
	$ docker run -t -i -v path_to_Data_Context_on_your_computer:/data_context ouruser/funseq /bin/bash		$ docker run -t -i -v path_to_Data_Context_on_your_computer:/funseq2/data_context ouruser/funseq /bin/bash
	$ cd funseq2		$ cd funseq2
	$ ./funseq2.sh		$ ./funseq2.sh

Public: /* Docker Image Usage */

2015-06-10T22:07:06Z

Docker Image Usage

← Older revision		Revision as of 22:07, 10 June 2015
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	$ docker load < funseq2-docker.tar		$ docker load < funseq2-docker.tar
	* Run docker container		* Run docker container
	$ docker run -t -i -v /data_context ouruser/funseq /bin/bash		$ docker run -t -i -v path_to_Data_Context_on_your_computer:/data_context ouruser/funseq /bin/bash
	$ cd funseq2		$ cd funseq2
	$ ./funseq2.sh		$ ./funseq2.sh

Public: /* Docker Image Usage */

2015-06-10T22:01:48Z

Docker Image Usage

← Older revision		Revision as of 22:01, 10 June 2015
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	* Export docker image to your computer:		* Export docker image to your computer:
	$ docker load < funseq2-docker.tar		$ docker load < funseq2-docker.tar
	* Run docker container~~; please modify 'config.txt' to specify path to Data Context~~		* Run docker container
	$ docker run -t -i ouruser/funseq /bin/bash		$ docker run -t -i -v /data_context ouruser/funseq /bin/bash
	$ cd funseq2		$ cd funseq2
	$ ./funseq2.sh		$ ./funseq2.sh

Public at 21:27, 10 June 2015

2015-06-10T21:27:05Z

← Older revision		Revision as of 21:27, 10 June 2015
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	types and COSMIC), the recurrence information is shown here. ‘recurrent element(name\|coordinates):cancer type(recurrence information in this		types and COSMIC), the recurrence information is shown here. ‘recurrent element(name\|coordinates):cancer type(recurrence information in this
	cancer type)’. Recurrence information is separated by ‘,’.		cancer type)’. Recurrence information is separated by ‘,’.

			=Docker Image Usage=
			Please download Docker at https://www.docker.com/
			* Export docker image to your computer:
			$ docker load < funseq2-docker.tar
			* Run docker container; please modify 'config.txt' to specify path to Data Context
			$ docker run -t -i ouruser/funseq /bin/bash
			$ cd funseq2
			$ ./funseq2.sh

	=Building data context=		=Building data context=

Public: /* Variant Prioritization */

2015-06-10T21:22:16Z

Variant Prioritization

← Older revision		Revision as of 21:22, 10 June 2015
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	==D. Tool Usage==		==D. Tool Usage==
	$ cd funseq2-1.2/		$ cd funseq2-1.2/

	Please modify 'config.txt' to specify the path to Data Context.		Please modify 'config.txt' to specify the path to Data Context.

Public: /* Variant Prioritization */

2015-06-10T21:21:46Z

Variant Prioritization

← Older revision		Revision as of 21:21, 10 June 2015
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	Please make sure you have Perl 5 and up. </span><br>		Please make sure you have Perl 5 and up. </span><br>

	==B. Tool ~~installation~~==		==B. Tool Download==
	~~This is a PERL- and Linux/UNIX-based tool. At the command-line prompt, type the following. The purpose is to write the path of perl modules to your environment. <br>~~

	~~$ tar xvf funseq2.1.0.tar~~		This is a PERL- and Linux/UNIX-based tool. At the command-line prompt, type the following.
	~~$ cd funseq2~~-~~1.0~~/		$ tar xvf funseq2.1.2.tar
	~~$ cd Funseq2/~~
	~~$ perl Makefile~~.PL
	~~$ make~~
	~~$ make install~~
	~~If you don’t have~~ the ~~permission to modify the environment~~, ~~open the ‘.bashrc’ file and add~~ the following ~~to the end of the file. Then ‘source .bashrc’~~. ~~<br>~~
	~~PERL5LIB=~~$~~{PERL5LIB}: $path_of_the_tool/~~funseq2-1.~~0/Funseq2/lib~~
	~~export PERL5LIB~~

	==C. Pre-built Data Context==		==C. Pre-built Data Context==
	All of the data can be downloaded under ‘Downloads’ in the web server. ~~If you would like to use the data, please download and put them under ‘funseq2-1.0/data’~~		All of the data can be downloaded under ‘Downloads’ in the web server.

	==D. Tool Usage==		==D. Tool Usage==
	To display the usage of tool, type ‘./~~run~~.sh’. <br>		$ cd funseq2-1.2/

			Please modify 'config.txt' to specify the path to Data Context.

			To display the usage of tool, type ‘./funseq2.sh’. <br>
	* Usage : ./run.sh -f file -maf MAF -m <1/2> -inf <bed/vcf> -outf <bed/vcf> -nc -o path -g file -exp file		* Usage : ./run.sh -f file -maf MAF -m <1/2> -inf <bed/vcf> -outf <bed/vcf> -nc -o path -g file -exp file
	-cls file -exf <rpkm/raw> -p int -cancer cancer_type -s score -uw -ua user_annotations_directory		-cls file -exf <rpkm/raw> -p int -cancer cancer_type -s score -uw -ua user_annotations_directory

Public: /* Building data context */

2015-01-20T18:10:50Z

Building data context

← Older revision		Revision as of 18:10, 20 January 2015
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	* All of other files can be replaced with user-specific data. Please refer to the files under ‘data/’ to correctly format them.		* All of other files can be replaced with user-specific data. Please refer to the files under ‘data/’ to correctly format them.

			=Contact=
			Yao Fu at yao DOT fu AT yale DOT edu